Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1180 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0222742146 sf0222736277 2 22742146 1.05E-30 1.37E-21
vg0131773460 sf0131772416 1 31773460 1.29E-12 NA
vg0826130413 sf0826127699 8 26130413 1.09E-11 NA
vg0912077331 sf0912076330 9 12077331 1.14E-11 NA
vg0809349508 sf0809348512 8 9349508 1.38E-11 NA
vg0225096894 sf0225091025 2 25096894 6.73E-10 3.33E-07
vg0205295866 sf0205295864 2 5295866 1.75E-09 2.66E-06
vg1217798287 sf1217769721 12 17798287 1.46E-08 NA
vg0335267908 sf0335260777 3 35267908 9.80E-08 NA
vg0222656032 sf0222650163 2 22656032 2.38E-07 9.00E-09
vg0317039059 sf0317037933 3 17039059 8.03E-07 8.58E-07
vg0600544519 sf0600543520 6 544519 2.15E-06 NA
vg1215653812 sf1215651109 12 15653812 NA 3.15E-06
vg0526678079 sf0526615437 5 26678079 NA 3.80E-06
vg0110176224 sf0110175200 1 10176224 NA 4.25E-06
vg0915181122 sf0915180121 9 15181122 NA 6.94E-06